From 43e3a5e060d6b3504e2d7f2c6eaff27698ce862a Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Tue, 10 Nov 2020 21:06:44 -0600
Subject: [PATCH] Address typo's and refernces to pipeline.
---
docs/references.md | 4 +---
docs/software_references_mqc.yaml | 5 ++---
docs/software_versions_mqc.yaml | 4 ++--
workflow/scripts/generate_versions.py | 4 ++--
4 files changed, 7 insertions(+), 10 deletions(-)
diff --git a/docs/references.md b/docs/references.md
index 2334436..4ea1690 100644
--- a/docs/references.md
+++ b/docs/references.md
@@ -16,9 +16,7 @@
* trimgalore [https://github.com/FelixKrueger/TrimGalore](https://github.com/FelixKrueger/TrimGalore)
6. **hisat2**:
- * Kim ,D.,Paggi, J.M., Park, C., Bennett, C., Salzberg, S.L. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019 Aug;37(8):907-915. doi: 10.1038/s41587-019-0201-4.
-
- Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. 2019 Nat Biotechnol. Aug;37(8):907-915. doi:[10.1038/s41587-019-0201-4](https://doi.org/10.1038/s41587-019-0201-4).
+ * Kim ,D.,Paggi, J.M., Park, C., Bennett, C., Salzberg, S.L. 2019 Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. Aug;37(8):907-915. doi:[10.1038/s41587-019-0201-4](https://doi.org/10.1038/s41587-019-0201-4).
7. **samtools**:
* Li H., B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis, R. Durbin, and 1000 Genome Project Data Processing Subgroup. 2009. The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics 25: 2078-9. doi:[10.1093/bioinformatics/btp352](http://dx.doi.org/10.1093/bioinformatics/btp352)
diff --git a/docs/software_references_mqc.yaml b/docs/software_references_mqc.yaml
index 669bb6f..675745f 100644
--- a/docs/software_references_mqc.yaml
+++ b/docs/software_references_mqc.yaml
@@ -4,7 +4,7 @@
description: 'This section describes references for the tools used.'
plot_type: 'html'
data: |
-
+
<h3 id="references">References</h3>
<ol style="list-style-type: decimal">
<li><strong>python</strong>:</li>
@@ -41,9 +41,8 @@
<li><strong>hisat2</strong>:</li>
</ol>
<ul>
- <li>Kim ,D.,Paggi, J.M., Park, C., Bennett, C., Salzberg, S.L. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019 Aug;37(8):907-915. doi: 10.1038/s41587-019-0201-4.</li>
+ <li>Kim ,D.,Paggi, J.M., Park, C., Bennett, C., Salzberg, S.L. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. 2019 Nat Biotechnol. 2019 Aug;37(8):907-915. doi:<a href="https://doi.org/10.1038/s41587-019-0201-4">10.1038/s41587-019-0201-4</a></li>
</ul>
- <p>Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. 2019 Nat Biotechnol. Aug;37(8):907-915. doi:<a href="https://doi.org/10.1038/s41587-019-0201-4">10.1038/s41587-019-0201-4</a>.</p>
<ol start="7" style="list-style-type: decimal">
<li><strong>samtools</strong>:</li>
</ol>
diff --git a/docs/software_versions_mqc.yaml b/docs/software_versions_mqc.yaml
index 8f228ac..6da4575 100644
--- a/docs/software_versions_mqc.yaml
+++ b/docs/software_versions_mqc.yaml
@@ -1,9 +1,9 @@
id: 'Software Versions'
section_name: 'Software Versions'
- section_href: 'https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/'
+ section_href: 'https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/78-tool_version/docs/RNA-Seq%20Pipeline%20Design%20Process%20Table.pdf'
plot_type: 'html'
- description: 'are collected at run time from the software output.'
+ description: 'are collected for pipeline version.'
data: |
<dl class="dl-horizontal">
diff --git a/workflow/scripts/generate_versions.py b/workflow/scripts/generate_versions.py
index 1ae7840..e191fd0 100644
--- a/workflow/scripts/generate_versions.py
+++ b/workflow/scripts/generate_versions.py
@@ -125,9 +125,9 @@ def main():
'''
id: 'Software Versions'
section_name: 'Software Versions'
- section_href: 'https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/'
+ section_href: 'https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/78-tool_version/docs/RNA-Seq%20Pipeline%20Design%20Process%20Table.pdf'
plot_type: 'html'
- description: 'are collected at run time from the software output.'
+ description: 'are collected for pipeline version.'
data: |
<dl class="dl-horizontal">
'''
--
GitLab